Hey Matt – my friend and I are also researching JMT options for 2016. Horseshoe Meadows is above 10,000′, so it’s a higher start, and you’d be hiking over 12,000 passes on the first day to access the JMT, depending on your route.
To acclimatize, you could start your hike someplace lower and a few days away from the southern JMT, such as Kennedy Meadows. Alternatively, you could day hike for two days first, being sure to sleep at a moderate elevation, such as camping at Mamoth Lakes or Tuolumne Meadows between 7,000′ – 9,000′). Of course, being in shape, being well hydrated, taking it easy the first few days, and knowing how your body reacts to altitude all help too.